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Human phosphoglycerate kinase in complex with ATP and 3PG formed by cross-soaking a TSA crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WZB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 MgF3 TSA complex crystals were formed from 50 mM Tris (pH 7.5), 20 mM DTT, 25 mM MgCl2, 50 mM 3PG, and 10 mM ADP supplemented with 20 mM NH4F and 1 mM deferoxamine, in 28-33% PEG 2000 MME and 0.1 M Bis/Tris pH 6.5. These were cross-soaked in 35% PEG 2000 MME; 0.1 M Bis/Tris pH 6.5, 20 mM DTT, 2.5mM EDTA, 10mM ATP and 50 mM 3PG
Crystal Properties Matthews coefficient Solvent content 2.15 42.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.04 α = 90 b = 91.1 β = 90 c = 108.2 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 83 PIXEL DECTRIS EIGER2 XE 16M 2016-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.58 54.1 99.9 0.033 0.047 0.033 0.999 12 2 53778 20.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.64 99.9 0.635 0.898 0.635 0.483 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.58 54.1 1.34 53773 2000 99.9 0.1795 0.1785 0.1834 0.2045 0.1759
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.221 f_angle_d 1.242 f_chiral_restr 0.059 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3116 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement xia2 data scaling DIALS data reduction PHENIX phasing